Glossary

We grouped here common terms used in integrative cancer biology. They are alphabetically listed for your convenience. We included a succinct definition for each term, which was thought as a very basic introduction to cancer biology-related as well as mathematics terms. This list is by no mean intended to be exhaustive and we will add more terms as we are updating our website.

Cancer Biology

• Angiogenesis refers to the process of forming new blood vessels. It is particularly critical for a tumor to promote angiogenesis in order to get the nutrients (such as oxygen) it needs to keep growing.
• Codon: three nucleotides forming a “three-letter word” which are used to code for amino acid (genetic code). There are 4 special codons: 1 start codon (ATG) and 3 stop codons (TAA, TAG, and TGA).
• Cytoplasm is, simply speaking, everything a cell contains, but the nucleus. It contains all the protein machinery (enzymes, cytoskeleton, organelles, etc).
• DNA stands for deoxyribonucleic acid. It is considered as the blueprint of life since it contains the coding information for all proteins (genes). It forms a double helix (2 complimentary strands) through the association of nucleotides (adenine-cytosine [A-T] or  guanine-thymine [G-C]). Only one strand is transcribed (5’->3’). DNA will condense into chromosomes prior to cell division.
• Eukaryotes are organisms in which genetic material is contained inside a membrane-bound nucleus.
• Genomics concerns the study of all the individual genes (genome) to decipher their functions and roles. More than the traditional molecular biology studies of genes, the introduction of microarrays and bioinformatics scaled up the type of research into being able to handle thousands of genes at once. For the past decade, genomics referred to the sequencing of whole organism genomes.
• In silico was created in reference to in vitro / in vivo, it refers to computer simulation. It is worth noting that ‘in silico’ has no meaning in Latin, compared to in vivo and in vitro.
• In vitro originally referred to experiment in a test tube, it is today generally applied to anything done in a controlled environment, outside a living organism.
• In vivo refers to research experiments done in a whole, living organism. Animal testing and clinical trials are forms of in vivo research.
• Invasion: in the cancer research field, it is synonymous of cell migration in the context of cells having broken of the primary site, moved through blood or lymphatic vessels, and “invading” normal tissue elsewhere to form secondary tumors.
• Metastasis: although the original location of a tumor is called “primary site”, metastasis refers to the spread of this tumor to secondary sites. It happens when cells from the original tumor break away, penetrate lymphatic or blood vessels, and invade a distant location.
• Migration is the process by which a cell moves. Although it is a very vital phenomenon (embryonic development, wound healing, immune responses, …), it is a cause of many diseases when deregulated. In cancer, up-regulated cell migration occurs in tumor formation and metastases.
• Nucleus is defined by a membrane, it contains all the genetic material of eukaryote cells.
• Oncogene is a gene that, if modified, will increase the malignancy of a cancerous cell. Some of them are critical in cancer development since their modification will increase the chance of a normal cell to become malignant. The first infamous oncogene discovered was src. The normal form of the gene is called proto-oncogene while its modified version is called oncogene.
• Prokaryotes: organisms without cell nucleus. This category mostly contains bacteria.
• Proliferation, also called “cell growth”, refers to the reproduction of cells. this is a complex and controlled process that is often found deregulated in cancer in which cells endlessly reproduce.
• Proteins are formed of amino acids. There are 20 amino acids but they can be further chemically-altered (“post-translational modifications”) into the estimated 100,000 different proteins present in the human body.
• Proteomics refers to the large-scale study of proteins that could answer the questions about their structure and function. The upper level in proteomics will integrate all protein structures and functions in order to map the entire cell signaling.
• RNA stands for ribonucleic acid. It is obtained after the transcription of DNA. Transferred in the cytoplasm, it is then translate into protein. While DNA is formed of A, T, G, and C nucleotides, RNA is formed of A, U , G, and C nucleotides. RNA are mostly found as single strand structure.
• Signaling pathway refers to the complex way communication takes place in a cell to coordinate its actions. It usually  involves many proteins with each possibly being found in different states (the simplest being “on”/”off” type). Through signaling pathways, a cell can monitor its environment and respond to it. In many diseases, including cancer, there are numerous errors in many signaling pathways that could account for a cell to become abnormal.
• Transcription is a process happening in the cell nucleus (for eukaryotes) or in the cytoplasm (prokaryotes) by which a DNA sequence (gene) is used to produce a complimentary RNA sequence.
• Translation is a process taking place in the cytoplasm by which a RNA sequence is used to assemble an amino acids sequence (protein). The RNA sequence starts with an initiation codon and ends with a stop codon.
• Tumor is referring to an abnormal growth of a tissue. Nowadays, it is synonymous of cancer or neoplasm.
• Tumor suppressor gene is a gene that reduces the chance of a cell to become cancerous. If it becomes mutated or deleted, the probability of a tumor transformation of the cell raises. The first tumor suppressor gene discovered was pRb. Another infamous example in this category is the gene p53.

Mathematics

terms compiled from the VICBC website

• a Differential Equation is an equation in which the derivatives (instantaneous rate of change) of a function appear as variables. Many of the fundamental laws of physics, chemistry, biology and economics can be formulated as differential equations. We often encounter a number of different types of differential equations while working with problems in biology and biophysics. The two most commonly used types are:
• An ordinary differential equation (ODE) only contains functions of one independent variable, and derivatives in that variable.
• A partial differential equation (PDE) contains functions of multiple independent variables and their partial derivatives.
• Non-Linear Processes, mathematically speaking, represent processes. whose behavior is not expressible as a sum of the behaviors of its descriptors. When an equation can be expressed in linear form, it becomes particularly easy to solve because it can be broken down into smaller pieces that may be solved individually.
• Equilibrium and non-equilibrium processes are, from a chemistry point of view, processes such that both the forward and reverse process of any chemical reaction occurs at equal rates. In other words, the concentrations are independent of time. In physics, and particularly in mechanics, equilibrium is often referred to a state where the sum of all the forces acting is zero. In other words, equilibrium defines a state where all forces (regardless of the nature of the forces) balance each other. On the other hand, non-equilibrium processes (especially in the context of chemistry and thermodynamics) have a dependence on time. Processes such as cell migration are examples of equilibrium processes.
• The (Thermodynamic) Stability of a biological system is often described in terms of its “free energy” or more specifically “Gibbs Free Energy”. The term measures the tendency of the system to react or change. The processes, for which the free energy is negative, are called “spontaneous” processes, whereas processes with positive free energy are not favored. So if we want to make a system more stable, we would like it to have more negative free energy, so that any change would only result in making the free energy for the process positive, and hence will be resisted. The free energy depends upon three parameters, the temperature, entropy (measure of the disorder of the system) and enthalpy (which measures the heat content of a system).
• Stochastic process is, in simple terms, a process that involves chance or probability, or from a calculus perspective, involves random variables. Stochastic methods are often used in modeling biological systems since most biological processes involve certain degree of probability, it could be probability of interaction, binding, folding etc. Other common areas where stochastic methods are used routinely are stock markets and financial transactions which involve chance and other random factors.

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